stereoAlign 0.0.2

A toolkit package of batch effects removal

A toolkit for data integration

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Behold, a magnificent toolkit emerges, designed to seamlessly integrate the vast realm of data in the realm of single-cell genomics. Within its hallowed digital confines, this toolkit bestows upon researchers the power to harmoniously merge and analyze the intricate tapestry of cellular information. Crafted with meticulous care, this toolkit embodies the epitome of elegance and efficiency. It serves as a conduit, enabling the synthesis of diverse datasets from single-cell genomics experiments, unlocking new realms of knowledge and understanding. The power of data integration within this toolkit extends beyond mere aggregation. It empowers researchers to unravel the intricate web of cellular interactions, uncovering hidden patterns, identifying novel cell types, and discerning the complex dynamics that govern cellular behavior. Through its refined algorithms and advanced statistical techniques, this toolkit illuminates the path towards deeper insights and discoveries. It refines and enhances the quality of data, mitigating confounding factors and removing noise, thus unveiling the true essence of the cellular landscape. As the sun sets on the horizon of single-cell genomics, this toolkit emerges as a guiding beacon, illuminating the path towards a more comprehensive understanding of cellular complexity. Embrace its power and unlock the secrets hidden within the realm of single-cell genomics.

Dependence

Install

The stereoAlign python package is available on Pypi and can be installed through

pip install stereoAlign

Import stereoAlign in python

import stereoAlign

We created the python package called stereoAlign that uses scanpy to streamline the integration of single-cell datasets and evaluate the results. The package contains several modules for preprocessing an anndata object, running integration methods and evaluating the resulting using a number of metrics. Functions for the data integration methods are in stereoAlign.alignment or for short stereoAlign.alg and metrics are under stereoAlign.metrics.

Tutorials

Quick Start https://stereoalign-tutorial.readthedocs.io/en/latest/index.html#

Integration Tools

This repository contains the code for the stereoAlign package for data integration tools.
This toolkit that is compared include:

Integration Method	Invoke	Describe
Harmony	stereoAlign.alg.harmony_alignment	Harmony wrapper function based on harmony-pytorch https://github.com/lilab-bcb/harmony-pytorch
Scanorama	stereoAlign.alg.scanorama_alignment	Scanorama wrapper function based on scanorama https://github.com/brianhie/scanorama
scGEN	stereoAlign.alg.scgen_alignment	scGen wrapper function based on scgen https://github.com/theislab/scgen with parametrization taken from the tutorial notebook https://scgen.readthedocs.io/en/stable/tutorials/scgen_batch_removal.html.
scvi	stereoAlign.alg.scvi_alignment	scVI wrapper function based on scvi-tools version >=0.16.0 (available through https://docs.scvi-tools.org/en/stable/installation.html)
MNN	stereoAlign.alg.mnn_alignment	MNN wrapper function (mnnpy implementation) based on mnnpy package https://github.com/chriscainx/mnnpy
BBKNN	stereoAlign.alg.bbknn_alignment	BBKNN wrapper function based on bbknn package https://github.com/Teichlab/bbknn
Combat	stereoAlign.alg.combat_alignment	ComBat wrapper function (scanpy implementation) using scanpy implementation of Combat https://scanpy.readthedocs.io/en/stable/generated/scanpy.pp.combat.html
DESC	stereoAlign.alg.desc_alignment	DESC wrapper function based on desc package https://github.com/eleozzr/desc
More methods	Additional methods are being incorporated...

Metric

Metric Method	Invoke
ARI	stereoAlign.metrics.cal_ari
Graph connectivity	stereoAlign.metrics.cal_graph_connectivity
KBET	stereoAlign.metrics.cal_kbet
LISI	stereoAlign.metrics.cal_lisi
Silhouette	stereoAlign.metrics.cal_silhouette

Disclaimer

This is not an official product.